File formats
accepted by Dendroscope

NEWICK/PHYLIP format

Dendroscope can display trees where edges are labeled using square
brackets i.e. [...]. For example, the following tree has the label
"mammals" attached to the internal branch grouping the mouse and
human OTUs

((human,mouse)[mammals],frog);

Indeed, after adding labels to branches of a tree using Dendroscope,
the software uses square brackets in exactly this way if you export
the tree in NEWICK format.

However, Dendroscope cannot display trees where the implicit
branch ancestral to the root is labeled in this way. For
example, the following tree would not open in Dendroscope, due to
the [tetrapods] label at the root.

((human,mouse)[mammals],frog)[tetrapods];

Therefore, NEWICK format trees imported from other sources may need
to be edited before they can be viewed in Dendroscope - for example,
trees exported from TreeFam have the root labeled in this way - this
must be removed before the tree is examined in Dendroscope.

Dendroscope format

After making changes to the way a tree is represented in
Dendroscope, you can save a file in native Dendroscope format. When
opened by Dendroscope, this file will show the same tree that you
saved with the same formating etc. as when you saved it.

Dendroscope
Graphical User Interface (GUI)

The graphical user interface (GUI) for Dendroscope should look
similar to the image shown below. The following components of the
GUI are labeled

the Main Window - where the phylogeny/tree is viewed

the Menu Bar - providing a range of different options to
manipulate the view of the phylogeny

the Side Bar - provides a list of all the trees present in the
current file

the Toolbar - provides short-cuts to several of the more
commonly-used menu items

Context Menus - right mouse-click on different regions of the
screen to obtain additional options applied to the selected
region

nodes

edges

background (allows selection of all edges/nodes/labels)

Opening a File

There is more than one way to open a file

File->Open

Use the "Open Tree File" icon

and then select file to be opened using you operating system's menus

Displaying Taxa Labels -
IMPORTANT!

To help present a large phylogeny in an uncluttered way, by default
Dendroscope chooses to hide from view many of the taxa labels on a
tree (where the labels would be overlapping and thus difficult to
read) - this is controlled by the option:
View->Sparse Labels

However, if you are searching for a taxon-label corresponding to a
particular sequence of interest, this can be problematic: the label
you are looking for may have been hidden by Dendroscope.

Therefore, you will often want to switch off this option by simply
selecting the View->Sparse Labels option (if there is a
tick after the option, then labels are being hidden)

Switching Between
Different Tree Representations

There are two ways of doing this:

Choosing the appropriate "Tree Representation" icon from the
toolbar

Use the Tree menu

Rooted, scaled tree representation

To view a tree so that it is shown with a root, and with
branch-length information included in the representation, do
one of the following:

Tree->Draw Rectangular Phylogram (i.e. using the
"Tree" menu)

Choose the
Toolbar icon

Rooted, unscaled tree representation

This is the default representation on some versions of
Dendroscope
To view a tree so that it is shown with a root, but with
branch-length information ignored in the representation, do the
following:

Tree->Draw Rectangular Cladogram (i.e. using the
"Tree" menu)

Choose the Toolbar icon

"Typical" unrooted
representation

Tree->Draw Radial Phylogram (i.e. using the "Tree"
menu)

Choose the Toolbar icon

Selecting Branches/Nodes

Depending on the number of left mouse-clicks you give to a
branch/node you can select

one click - only the clicked-on branch

two clicks - the entire clan/subtree associated with one end
of the branch (including branches, nodes, and labels)

three clicks - the entire clan/subtree associated with the
other end of the branch (including branches, nodes, and labels)

Multiple branches/nodes/labels can be selected/de-selected by left
mouse-clicking while holding the SHIFT key. The image below shows
several branches, nodes, and labels highlighted.

Reroot Tree

Left-click with the mouse on the branch you want to
place the root on to select it and then either:

Select the "Reroot tree" Toolbar icon

Edit->Reroot

Rotate Branches
Around a Node

To rotate branches (which does not change the topology of the tree,
only the way it is represented)

Left-click with the mouse on the node (doesn't work
i.e. won't let you choose to "Swap Subtree etc. if you select a
branch instead of a node!) you want to rotate around to select
it and then either:

Select the "Swap order of subtrees below node" Toolbar icon

Edit->Swap Subtree

Right-click to obtain the node Context Menu and choose
"Swap Subtree"

Formatting Branches
and Nodes

To change the colour/thickness/font etc. of selected
nodes/branches/labels do:

Edit->Format

This brings up the "Format" window shown below

From here you can, for example:

change the width of branches by altering the "Edge Width"

change the colour of the selected nodes/branches/labels by
clicking on the colour pallet to choose the appropriate colour

change the size of the text used for the labels using the
middle-top menu-box (above this contains the number "10")

See the image below for an example of such editing.

Adding Labels to
Branches

It is possible to add text-labels to branches - for example to
supply the name of a clade - e.g. vertebrates - associated with a
particular group:

Select branch(es) of interest

Right-click to get access to the Branch Context Menu

Choose "Edit Edge Label" to provide a text-label for the
branch - any gaps in your text will be substituted by "_"
characters on the label

For example, the image below has a label added to the thick yellow
branch.

Adjusting Positions
of Labels

By simply left-clicking with the mouse and dragging it is possible
to change the position of any of the labels (either branch labels as
above, or the taxa labels at the end of branches. These labels
remain attached to their branches and will move accordingly
following rearrangements of the tree

Adding a scale bar

Saving a Tree
Representation

You can save the representation of your tree in a format that is
read only by Dendroscope - this file can be reloaded into
Dendroscope at a later date, and will have exactly the same set of
rearrangements and formating as the trees in Dendroscope when the
file was saved. You can do this using either of:

File->Save

File->Save As...

If you are looking to save the image for use in preparing a figure,
then use

File->Export Image

and save the file in either EPS or SVG format (to maintain
it as a set of vectors rather than reducing it to a set of pixels as
the other formats do)

The resulting file can then be loaded into a range of different
software such as Adobe Illustrator to prepare a file version of a
figure for publication/presentation

Hiding Branch/Edge
Annotations/Labels

Trees obtained from some sources, such as TreeFam, have information
annotated/associated with tree branches that can sometimes make the
shape, and other features, of the tree difficult to read/interpret.
Thus, if we're not interested in reading this information, we
usually turn off the representation of this information using the
"View" menu:

View->Hide Edge Labels

Below is an example of a tree with edge labels shown
And here with the labels hidden - this makes the tree topology and
other features of the tree much easier to read/identify

Changing angle of
branches in unrooted tree representation

To change the angle at which branches are drawn in the typical
unrooted tree representation: